We present the hexagonal digital moiré method for three-directional structural characterization of hexagonal packed nanostructures. A mismatch between a three-way grating and a nanoparticle assembly is shown to produce hexagonal moiré fringes due to the interference between three groups of parallel moiré patterns. The measuring principles of the pitches and the orientations of the three 1D arrays of the nanoparticles are presented. The structural information on a silica nanoparticle assembly is analyzed.